i'd like to point out that at the begining of the series whenever naruto used chakra he got an aura around him. now that he's learned more control he no longer gets a blue aura whenever doing a technique.

now, assuming that the wasted chakra thing is true, it can be assumed that anruto is simply able to be entirely efficient when using the nine tails chakra. perhaps at some point in the future he'll gain enough control not to waste any.